"obgen" - Generate Molecule 3D Structures

Cheminformatics Tutorials - Herong's Tutorial Examples

∟Command Line Tools Provided by Open Babel

∟"obgen" - Generate Molecule 3D Structures

This section provides a quick introduction on the 'obgen' command provided in Open Babel package to generate molecule 3D structure.

What Is "obgen" command? - "obgen" command is a command line tool provided in the Open Babel package that allows you to Generate Molecule 3D Structures. "obgen" command does the same job as the "obabel ... --gen3D" with more options.

Here is the user manual of the "obgen" command.

NAME
     obgen -- generate 3D coordinates for a molecule

SYNOPSIS
     obgen [OPTIONS] filename

DESCRIPTION
     The obgen tool will generate 3D coordinates for molecules in a file (e.g. 
     multi-molecule SMILES files). The resulting structure will be optimized 
     using the given forcefield and checked for the lowest-energy conformer
     using a Monte Carlo search.  Output will be sent to standard output in 
     the SDF file format.

OPTIONS
     If no filename is given, obgen will give all options including the available 
     forcefields.

     -ff forcefield
           Select the forcefield

EXAMPLES
     View the possible options, including available forcefields:
           obgen

     Generate 3D coordinates for the molecule(s) in file test.smi:
           obgen test.smi

     Generate 3D coordinates for the molecule(s) in file test.smi using the UFF forcefield:
           obgen -ff UFF test.smi

Here is an example of generating, or converting, a given molecule structure to the best conforming 3D structure using the default force field type:

1. Create a 2D structure of the tyrosine molecule:

herong$ obabel "-:c1cc(ccc1CC(C(=O)O)N)O" -O tyrosine.sdf --gen2D
1 molecule converted

herong$ obabel tyrosine.sdf tyrosine.svg
1 molecule converted
29 audit log messages

2. Generate, or convert, the 2D structure to 3D structure using the "obgen" command:

herong$ obgen tyrosine.sdf > tyrosine-3d-obgen.sdf 

A T O M   T Y P E S
IDX  TYPE
1  37
2  37
3  37
...

F O R M A L   C H A R G E S
IDX  CHARGE
1  0.000000
2  0.000000
3  0.000000
...

P A R T I A L   C H A R G E S
IDX  CHARGE
1  -0.150000
2  -0.150000
3  0.082500
...

S E T T I N G   U P   C A L C U L A T I O N S

SETTING UP BOND CALCULATIONS...
SETTING UP ANGLE & STRETCH-BEND CALCULATIONS...
SETTING UP TORSION CALCULATIONS...
SETTING UP OOP CALCULATIONS...
SETTING UP VAN DER WAALS CALCULATIONS...
SETTING UP ELECTROSTATIC CALCULATIONS...

S T E E P E S T   D E S C E N T
STEPS = 500
STEP n       E(n)         E(n-1)    
------------------------------------
    0     124.930      ----
   10    43.09167    44.83204
   20    29.55319    29.87195
   30    20.14396    22.92951
   ...
    STEEPEST DESCENT HAS CONVERGED

W E I G H T E D   R O T O R   S E A R C H
  NUMBER OF ROTATABLE BONDS: 3
  NUMBER OF POSSIBLE ROTAMERS: 288
  INITIAL WEIGHTING OF ROTAMERS...

  GENERATED 250 CONFORMERS
CONFORMER     ENERGY
--------------------
     1        11.188
     2         4.809
     3         3.506
     ..           ...
   248         6.265
   249        11.152
   250         9.037

  LOWEST ENERGY:    0.926

S T E E P E S T   D E S C E N T
STEPS = 500
STEP n       E(n)         E(n-1)    
------------------------------------
    0       0.926      ----
   10     0.92061     0.92084
   20     0.91410     0.91561
   30     0.90976     0.91002
   ... 
     STEEPEST DESCENT HAS CONVERGED

herong$ obabel tyrosine-3d-obgen.sdf tyrosine-3d-obgen.svg -d 
1 molecule converted
34 audit log messages

You need a 3D structure viewer to see the 3D structure. But you can look at the 2D presentation of the 3D structure.

Tyrosine Molecule 3D Structure Generated from 'obgen'

3. You can actually use "obabel ... --gen3D" command to do same job as the "obgen" command. The result is the same as the "obgen" command.

herong$ obabel tyrosine.sdf tyrosine-3d-babel.sdf --gen3D 
1 molecule converted

herong$ obabel tyrosine-3d-babel.sdf tyrosine-3d-babel.svg -d 
1 molecule converted

Tyrosine Molecule 3D Structure Generated from 'babel'

4. Or you can generate the 3D structure from the SMILES string directly using the "obabel" command. The result is almost the same as the "obgen" command.

herong$ obabel "-:c1cc(ccc1CC(C(=O)O)N)O" -O tyrosine-3d-def.sdf --gen3D
1 molecule converted

herong$ obabel tyrosine-3d-def.sdf tyrosine-3d-def.svg -d 
1 molecule converted
34 audit log messages